From f9c7c7099a20091b47f90cfea056fba80e4b10ea Mon Sep 17 00:00:00 2001 From: Dung Truong Date: Thu, 7 Oct 2021 20:58:17 -0700 Subject: [PATCH] make it work with STUDY --- eegplugin_bids.m | 4 +-- pop_eventinfo.m | 80 +++++++++++++++++++++++------------------------- 2 files changed, 41 insertions(+), 43 deletions(-) diff --git a/eegplugin_bids.m b/eegplugin_bids.m index 9653919..e31996d 100644 --- a/eegplugin_bids.m +++ b/eegplugin_bids.m @@ -44,8 +44,8 @@ % create BIDS menus % ----------------- comtaskinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_taskinfo(EEG);' catchstrs.store_and_hist ]; - comsubjinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_participantinfo(EEG,STUDY);' catchstrs.store_and_hist ]; - comeventinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_eventinfo(EEG);' catchstrs.store_and_hist ]; + comsubjinfo = [trystrs.no_check '[EEG,STUDY,LASTCOM] = pop_participantinfo(EEG,STUDY);' catchstrs.store_and_hist ]; + comeventinfo = [trystrs.no_check '[EEG,STUDY,LASTCOM] = pop_eventinfo(EEG,STUDY);' catchstrs.store_and_hist ]; % comvalidatebids = [ trystrs.no_check 'if plugin_askinstall(''bids-validator'',''pop_validatebids'') == 1 pop_validatebids() end' catchstrs.add_to_hist ]; bids = findobj(fig, 'label', 'BIDS tools'); if isempty(bids) diff --git a/pop_eventinfo.m b/pop_eventinfo.m index 8cef76f..006361f 100644 --- a/pop_eventinfo.m +++ b/pop_eventinfo.m @@ -14,29 +14,36 @@ % 'EEG' - [struct] Updated EEG structure containing event BIDS information % in each EEG structure at EEG.BIDS.eInfoDesc and EEG.BIDS.eInfo % -% 'eInfoDesc' - [struct] structure describing BIDS event fields as you specified. +% 'eInfoDesc' - [struct] structure describing BIDS event fields as you specified. % See BIDS specification for all suggested fields. % -% 'eInfo' - [cell] BIDS event fields and their corresponding +% 'eInfo' - [cell] BIDS event fields and their corresponding % event fields in the EEGLAB event structure. Note that % EEGLAB event latency, duration, and type are inserted % automatically as columns "onset" (latency in sec), "duration" % (duration in sec), "value" (EEGLAB event type) % % Author: Dung Truong, Arnaud Delorme -function [EEG, command] = pop_eventinfo(EEG, varargin) +function [EEG, STUDY, command] = pop_eventinfo(EEG, STUDY, varargin) %% check if there's already an opened window if ~isempty(findobj('Tag','eventBidsTable')) errordlg2('A window is already openened for pop_eventinfo'); return end - command = '[EEG, command] = pop_eventinfo(EEG)'; + command = '[EEG, [], command] = pop_eventinfo(EEG)'; + %% if STUDY is provided, check for consistency + hasSTUDY = false; + if exist('STUDY','var') && ~isempty(STUDY) + [STUDY, EEG] = pop_checkdatasetinfo(STUDY, EEG); + command = '[EEG, STUDY, command] = pop_eventinfo(EEG, STUDY);'; + hasSTUDY = true; + end + % perform check to make sure EEG.event is consistent across EEG if isempty(EEG(1).event) errordlg2('EEG.event is empty for first dataset'); - return - + return end try eventFields = fieldnames([EEG.event]); @@ -48,7 +55,7 @@ warning('There is mismatch in number of fields in EEG.event structures. Using fields of EEG(%d) which has the highest number of fields (%d).', index, num); end end - bidsFields = {'onset', 'duration', 'trial_type','value','stim_file','sample','response_time'};%,'HED'}; + bidsFields = {'onset', 'duration', 'trial_type','value','stim_file','sample','response_time'}; eventFields = setdiff(eventFields, 'latency'); % define global variables % ----------------------- @@ -63,7 +70,7 @@ fontSize = 12; % Use GUI - if nargin < 2 + if nargin < 3 % create UI f = figure('MenuBar', 'None', 'ToolBar', 'None', 'Name', 'Edit BIDS event info - pop_eventinfo', 'Color', bg); f.Position(3) = appWidth; @@ -110,7 +117,7 @@ if isfield(eventBIDS.(field), 'Levels') && ~isempty(eventBIDS.(field).Levels) data{i,strcmp(tbl.ColumnName, 'Levels')} = strjoin(fieldnames(eventBIDS.(field).Levels),','); else - if strcmp(field, 'onset') || strcmp(field, "sample") || strcmp(field, "duration") || strcmp(field, "HED") + if strcmp(field, 'onset') || strcmp(field, "sample") || strcmp(field, "duration") data{i,strcmp(tbl.ColumnName, 'Levels')} = 'n/a'; else data{i,strcmp(tbl.ColumnName, 'Levels')} = 'Click to specify below'; @@ -122,7 +129,7 @@ tbl.Data = data; waitfor(f); % Use default value - pop_eventinfo(EEG,'default') called - elseif nargin < 3 && ischar(varargin{1}) && strcmp(varargin{1}, 'default') + elseif nargin < 4 && ischar(varargin{1}) && strcmp(varargin{1}, 'default') done(); end @@ -201,8 +208,12 @@ function done() % prepare return struct fields = fieldnames(eventBIDS); - if isfield(EEG.etc,'tags') - hedTags = EEG.etc.tags; + fMap = []; + if hasSTUDY && isfield(STUDY.etc, 'tags') + hedTags = STUDY.etc.tags; + fMap = fieldMap.createfMapFromStruct(hedTags); + elseif isfield(EEG(1).etc,'tags') + hedTags = EEG(1).etc.tags; fMap = fieldMap.createfMapFromStruct(hedTags); end for k=1:length(fields) @@ -229,18 +240,23 @@ function done() if isfield(eventBIDS.(bidsField),'Levels') && ~isempty(eventBIDS.(bidsField).Levels) && ~strcmp(eventBIDS.(bidsField).Levels,'n/a') eInfoDesc.(bidsField).Levels = eventBIDS.(bidsField).Levels; end - % parse HED - if isfield(EEG.etc,'tags') + % parse HED if exists + if ~isempty(fMap) tMap = fMap.getMap(eegField); - if ~isempty(tMap) + if ~isempty(tMap) && tMap.hasAnnotation() codes = tMap.getCodes(); if numel(codes) == 1 && strcmp(codes{1},'HED') tList = tMap.getValue('HED'); - eInfoDesc.(bidsField).HED = tagList.stringify(tList.getTags()); + if tList.hasAnnotation() + eInfoDesc.(bidsField).HED = tagList.stringify(tList.getTags()); + end else for c=1:numel(codes) tList = tMap.getValue(codes{c}); - eInfoDesc.(bidsField).HED.(codes{c}) = tagList.stringify(tList.getTags()); + % only add HED tags for the ones that + if tList.hasAnnotation() + eInfoDesc.(bidsField).HED.(codes{c}) = tagList.stringify(tList.getTags()); + end end end end @@ -250,12 +266,12 @@ function done() end end end - if numel(EEG) == 1 - command = '[EEG, eInfoDesc, eInfo] = pop_eventinfo(EEG);'; - else - command = '[EEG, eInfoDesc, eInfo] = pop_eventinfo(EEG);'; - end + % add info to STUDY if exists + if hasSTUDY + STUDY.BIDS.eInfoDesc = eInfoDesc; + STUDY.BIDS.eInfo = eInfo; + end % add info to EEG structs for e=1:numel(EEG) EEG(e).BIDS.eInfoDesc = eInfoDesc; @@ -380,9 +396,7 @@ function createLevelUI(~,~,table,field) removeLevelUI(); matchedRow = strcmp(table.Source.Data(:, strcmp(table.Source.ColumnName, 'BIDS Field')), field); levelCellText = table.Source.Data{matchedRow, strcmp(table.Source.ColumnName, 'Levels')}; % text @ (field, Levels) cell. if 'n/a' then no action, 'Click to..' then conditional action, ',...' then get levels - if strcmp(field, 'HED') - uicontrol(f, 'Style', 'text', 'String', 'Levels editing not applied for HED. Use ''pop_tageeg(EEG)'' of HEDTools plug-in to edit event HED tags', 'Units', 'normalized', 'Position', [0.01 0.45 1 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg'); - elseif strcmp(field, 'onset') || strcmp(field, 'sample') || strcmp(field, 'duration') + if strcmp(field, 'onset') || strcmp(field, 'sample') || strcmp(field, 'duration') uicontrol(f, 'Style', 'text', 'String', 'Levels editing not applied for field with continuous values.', 'Units', 'normalized', 'Position', [0.01 0.45 1 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg'); else % retrieve all unique values from EEG.event.(field). @@ -619,23 +633,7 @@ function removeLevelUI() event.value.Units = ''; event.value.Levels = []; event.value.TermURL = ''; -% elseif strcmp(fields{idx}, 'HED') && any(strcmp(eventFields, 'usertags')) -% if isfield(EEG(1).event, 'usertags') -% event.HED.EEGField = 'usertags'; -% else -% event.HED.EEGField = ''; -% end -% event.HED.LongName = 'Hierarchical Event Descriptor'; -% event.HED.Description = 'Tags describing the nature of the event'; -% event.HED.Levels = []; -% event.HED.Units = ''; -% event.HED.TermURL = ''; elseif strcmp(fields{idx}, 'duration') -% if isfield(EEG(1).event, 'duration') -% event.HED.EEGField = 'duration'; -% else -% event.HED.EEGField = ''; -% end event.duration.LongName = 'Event duration'; event.duration.Description = 'Duration of the event (measured from onset) in seconds. Must always be either zero or positive. A "duration" value of zero implies that the delta function or event is so short as to be effectively modeled as an impulse.'; event.duration.Units = 'second';